Search Results (4,943)

 Lbx1 plays important roles in different processes, including the development of sensory pathways, neuronal cell fate regulation, and muscle cell precursor migration. Genetic variation in the LBX1 locus has been associated with several human disease conditions, such as idiopathic scoliosis, congenital limb malformation, and neuropsychiatric illness, including attention-deficit/hyperactivity disorder (ADHD) and anxiety disorders. Zebrafish (Danio rerio) were used to investigate the behavioral consequences of the loss of function of the two orthologs to the human LBX1 gene, zebrafish lbx1a and lbx1b. We observed a consistent locomotor hyperactivity phenotype induced by a novel environment in lbx1a mutants. Repeated dark stimuli provoked similar responses in both mutant lines, including the novelty-induced hyperactivity. We performed RNAseq on total RNA isolated from the head region of mutant and wildtype larvae. Several differentially expressed genes were identified, giving more insights into Lbx1 target genes and pathways, which could be relevant regarding the evaluation of zebrafish lbx1a or lbx1b as a human disease model. Furthermore, the analysis was complemented with a comparison to the expression profile of human LBX1 overexpression in cell culture, revealing a convergence on just two commonly regulated genes, namely alpha-Internexin (INA) and Fibrillin-3 (FBN3). In conclusion, our findings might further elucidate the multitude of functions of Lbx1 and its involvement in various human disease conditions.  Full article

Astrocytes and microglia constitute nearly half of all central nervous system cells and are indispensable for its proper function. Both exhibit striking morphological and functional heterogeneity, adopting either neuroprotective (A2, M2) or proinflammatory (A1, M1) phenotypes in response to cytokines, pathogen-associated molecular patterns (PAMPs)/damage-associated molecular patterns (DAMPs), toll-like receptor 4 (TLR4) activation, and NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome signaling. Crucially, many of these phenotypic transitions arise during the earliest stages of neurodegeneration, when glial dysfunction precedes overt neuronal loss and may act as a primary driver of disease onset. This review critically examines glial-centered hypotheses of neurodegeneration, with emphasis on their roles in early disease phases: (i) microglial polarization from an M2 neuroprotective state to an M1 proinflammatory state; (ii) NLRP3 inflammasome assembly via P2X purinergic receptor 7 (P2X7R)-mediated K⁺ efflux; (iii) a self-amplifying astrocyte–microglia–neuron inflammatory feedback loop; (iv) impaired microglial phagocytosis and extracellular-vesicle–mediated propagation of β-amyloid (Aβ) and tau; (v) astrocytic scar formation driven by aquaporin-4 (AQP4), matrix metalloproteinase-9 (MMP-9), glial fibrillary acidic protein (GFAP)/vimentin, connexins, and janus kinase/signal transducer and activator of transcription 3 (JAK/STAT3) signaling; (vi) cellular reprogramming of astrocytes and NG2 glia into functional neurons; and (vii) mitochondrial dysfunction in glia, including Dynamin-related protein 1/Mitochondrial fission protein 1 (Drp1/Fis1) fission imbalance and dysregulation of the sirtuin 1/peroxisome proliferator-activated receptor gamma coactivator 1-alpha (Sirt1/PGC-1α) axis. Promising therapeutic strategies target pattern-recognition receptors (TLR4, NLRP3/caspase-1), cytokine modulators (interleukin-4 (IL-4), interleukin-10 (IL-10)), signaling cascades (JAK2–STAT, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), phosphoinositide 3-kinase–protein kinase B (PI3K–AKT), adenosine monophosphate-activated protein kinase (AMPK)), microglial receptors (triggering receptor expressed on myeloid cells 2 (TREM2)/spleen tyrosine kinase (SYK)/ DNAX-activating protein 10 (DAP10), siglec-3 (CD33), chemokine C-X3-C motif ligand 1/ CX3C motif chemokine receptor 1 (CX3CL1/CX3CR1), Cluster of Differentiation 200/ Cluster of Differentiation 200 receptor 1 (CD200/CD200R), P2X7R), and mitochondrial biogenesis pathways, with a focus on normalizing glial phenotypes rather than simply suppressing pathology. Interventions that restore neuroglial homeostasis at the earliest stages of disease may hold the greatest potential to delay or prevent progression. Given the complexity of glial phenotypes and molecular isoform diversity, a comprehensive, multitargeted approach is essential for mitigating Alzheimer’s disease and related neurodegenerative disorders. This review not only synthesizes pathogenesis but also highlights therapeutic opportunities, offering what we believe to be the first concise overview of the principal hypotheses implicating glial cells in neurodegeneration. Rather than focusing on isolated mechanisms, our goal is a holistic perspective—integrating diverse glial processes to enable comparison across interconnected pathological conditions. Full article

Pediatric food allergies are an escalating public health concern, with nut allergies representing a primary cause of persistent hypersensitivity and anaphylaxis. New data suggests that pediatric populations with multiple nut allergies (MNA) may be at higher anaphylaxis risk than their counterparts with single nut allergies. Despite this, there is an absence of literature posing multiple nut allergies against singular nut allergy cases. The majority of the research in this topic is directed towards singular nut allergy, without any differentiation between children with one versus multiple sensitivities. Epidemiological evidence indicates that multiple nut allergies are associated with lifelong sensitization, high cross-reactivity potential and increased risk and severity of reactions. Compounding clinical risk factors reinforce the already high risk associated with MNA and indicate that these children require careful monitoring and individual management. Diagnostic tools, including component-resolved diagnostics and oral food challenges, enable differentiation between true multi-nut sensitization and cross-reactivity, guiding targeted interventions. Management strategies must therefore be multifaceted, encompassing selective allergen avoidance, emergency preparedness with epinephrine auto-injectors, asthma control, nutritional support, and psychosocial care. Recognizing MNA as a distinct, high-risk phenotype highlights the necessity of precision-based, biomarker-driven clinical approaches to optimize safety, reduce morbidity, and improve quality of life for affected pediatric populations. Full article

Background: Perianal involvement is a well-recognized manifestation of Crohn’s disease (CD). However, non-fistulizing perianal phenotypes remain underrecognized despite their significance in clinical practice and impact on patients’ quality of life. Methods: A narrative review of the literature up to September 2025 was conducted, with an emphasis on studies that differentiated between non-fistulizing and fistulizing lesions. Results: During the CD course, approximately 45% of patients with CD develop non-fistulizing perianal manifestations, including fissures, ulcers, strictures, and skin tags. These lesions may resolve spontaneously with the ongoing CD therapy or additional conservative measures, but some evolve into more complex conditions, with challenging management. Deep ulcers and strictures appear to be associated with a less favorable disease course. While biologic therapy has altered the overall course of CD, its role in treating non-fistulizing perianal Crohn’s disease (PCD) requires further understanding. Surgical intervention, which carries an increased risk of complications, is typically reserved for individuals who are refractory to other treatments. The potential association between non-fistulizing PCD and anal cancer remains uncertain. Conclusions: Non-fistulizing PCD is a clinically significant condition that requires early recognition and individualized management. Prospective studies with standardized lesion classification, careful monitoring of disease course, and evaluation of biologic therapies and biomarkers are needed to develop evidence-based strategies and improve patient outcomes on non-fistulizing PCD. Full article

Personalizing therapy using medical marijuana (MM) is based on understanding the pharmacogenomics (PGx) and drug–drug interactions (DDIs) involved, as well as identifying potential epigenetic risk markers. In this work, the evidence regarding the role of variants in phase I (CYP2C9, CYP2C19, CYP3A4/5) and II (UGT1A9/UGT2B7) genes, transporters (ABCB1), and selected neurobiological factors (AKT1/COMT) in differentiating responses to Δ⁹-tetrahydrocannabinol (THC) and cannabidiol (CBD) has been reviewed. Data indicating enzyme inhibition by CBD and the possibility of phenoconversion were also considered, which highlights the importance of a dynamic interpretation of PGx in the context of current pharmacotherapy. Simultaneously, the results of epigenetic studies (DNA methylation, histone modifications, and ncRNA) in various tissues and developmental windows were summarized, including the reversibility of some signatures in sperm after a period of abstinence and the persistence of imprints in blood. Based on this, practical frameworks for personalization are proposed: the integration of PGx testing, DDI monitoring, and phenotype correction into clinical decision support systems (CDS), supplemented by cautious dose titration and safety monitoring. The culmination is a proposal of tables and diagrams that organize the most important PGx–DDI–epigenetics relationships and facilitate the elimination of content repetition in the text. The paper identifies areas of implementation maturity (e.g., CYP2C9/THC, CBD-CYP2C19/clobazam, AKT1, and acute psychotomimetic effects) and those requiring replication (e.g., multigenic analgesic signals), indicating directions for future research. Full article

Among cardiomyopathies, the hypertrophic phenotype is the most common, and hypertrophic cardiomyopathy (HCM) phenocopies represent a heterogeneous group of conditions. They are defined by a left ventricular wall thickness ≥15 mm in the absence of other causes such as loading conditions, ischemia, or valvular disease. Although they mimic similar clinical and morphological features, their etiologies are distinct and include genetic, metabolic, and infiltrative mechanisms. Therefore, accurate classification and differential diagnosis are crucial for effective management and treatment. Sarcomeric HCM is the most frequent form, accounting for up to 60% of cases. However, numerous non-sarcomeric phenocopies exist, including amyloidosis, Fabry disease, glycogen storage disorders, RASopathies, and mitochondrial diseases. Clinical and imaging findings are essential to distinguish these entities from sarcomeric HCM. Electrocardiography, echocardiography, advanced modalities such as cardiac magnetic resonance (CMR), and specific laboratory tests all play a central role in guiding diagnosis. Genetic testing provides key insights into mutations and inheritance patterns, further supporting definitive diagnosis. Correct identification of an HCM phenocopy carries important therapeutic implications, as disease-specific treatments can significantly improve prognosis. For example, targeted therapies exist for amyloidosis, Fabry disease, and certain metabolic or mitochondrial disorders, underlining the clinical relevance of an accurate diagnosis. This review aims to provide an overview of HCM phenocopies and assist clinicians in diagnostic reasoning. The first part addresses classification according to pathophysiological mechanisms, clinical features, and genetic background. The second part focuses on the stepwise approach to differential diagnosis, integrating clinical assessment, laboratory evaluation, ECG, echocardiography, and CMR findings. Full article

Heat stress significantly impairs dairy cow health and productivity, highlighting the need to understand the gut microbiome–metabolite interactions that contribute to heat tolerance. Here, we integrated metagenomic sequencing and untargeted metabolomics in twelve holstein cows selected from a previously phenotyped herd of 120 individuals, including six heat-tolerant (HT) and six heat-sensitive (HS) cows identified using entropy-weighted TOPSIS scoring. HT cows were enriched in genera such as Faecalimonas and UBA737, which were functionally linked to pathways of energy and lipid metabolism, whereas, HS cows harbored taxa associated with bacterial lipopolysaccharide and glycosphingolipid biosynthesis. A total of 135 metabolites were differentially abundant between groups. Among them, glycerol 2-phosphate and 24(28)-dehydroergosterol showed perfect classification performance (AUC = 1.000), and were mainly involved in membrane lipid remodeling and redox regulation. Integrated analysis revealed coordinated microbial–metabolite networks, exemplified by the Faecalimonas–LysoPS (16:0/0:0) and UBA737–Glycerol 2-phosphate axes, suggesting functional coupling between microbial composition and metabolic adaptation. Together, these findings demonstrate that HT cows harbor gut microbiota and metabolites favoring energy balance, membrane remodeling, and oxidative stress resilience, while HS cows display stress-related metabolic patterns. This study elucidates the microbial–metabolic mechanisms underlying thermal resilience and highlights potential biomarkers and metabolic pathways that could be applied in heat-tolerance breeding and precision management of dairy cattle. Full article

Background: Chili pepper (Capsicum annuum L.), a globally cultivated and ancient domesticated crop, carries considerable significance in agriculture. While radiation-induced mutagenesis has found application in this crop, the mutagenic efficacy and molecular-level impacts of 7Li ion beam radiation remain poorly elucidated. Methods: We irradiated pepper with a beam of 7Li ions to create a mutant, which showed good economic traits, and phenotypic and physio-biochemical characterization were combined with proteomic and metabolomic profiling to delineate the mutagenic mechanisms. Quantitative real-time PCR (qRT-PCR) was further utilized to assess the biological impact and underlying response pathways. We used this to evaluate the biological impact and the reaction mechanisms behind it. Results: 7Li beam radiation positively influenced morphology and physiological traits, notably chlorophyll and anthocyanin content. Leveraging proteomic profiling detected 6082 proteins, including 355 differential proteins (139 upregulated, 216 downregulated), enriched in 4 KEGG pathways. Based on GO and KEGG network analysis, 250 metabolites were quantified, with 120 being differentially abundant (112 upregulated, 8 downregulated), enriched in 9 metabolic pathways. Furthermore, qRT-PCR results revealed that differentially expressed genes were consistent with the corresponding metabolomic data. Joint analysis revealed the coordinated enrichment of differential metabolites and proteins in pathways related to amino acid and carbohydrate metabolism. These findings suggest that these active pathways in pepper are related to its response to ion beam radiation. Overall, this study is a valuable resource for subsequent genomic research on peppers and 7Li ion beam radiation research. Full article

The intestine is a multifunctional organ responsible for digestion, nutrient absorption, metabolic regulation, and innate immunity. In flatworms, recent studies have highlighted the importance of intestine-enriched genes expressed strongly in cells of the digestive tract. These genes are not only involved in digestion, nutrient uptake, transport, metabolism, and feeding behavior, but also in the modulating dynamics of stem cells (neoblasts). In Macrostomum lignano, the molecular mechanisms regulating interaction between digestive and neural processes remain poorly understood, as in other free-living flatworms. Therefore, identifying the genes required for intestinal integrity and feeding behavior is essential for understanding the underpinning mechanisms. In this study, we examined intestine-enriched candidate genes predicted to be involved in cell differentiation and maintenance of the intestine in M. lignano and whether the knockdown of these genes affects other tissues’ functioning. Using RNAi-mediated gene silencing, we identified four genes (kri1, wbp2nl, Mlig-tuf1, and Mlig-tuf2) whose knockdown causes pronounced phenotypes, including reduced feeding, fasting behavior, decreased body size and cell proliferation, low reproduction, and altered expression of an intestine-specific apob promoter. We have characterized their roles in intestinal homeostasis and neoblast dynamics and discussed potential mechanisms linking gene disruption to changes in feeding behavior. Full article

Background: The immunoglobulin superfamily member 1 (IGSF1) gene encodes for a transmembrane glycoprotein involved in crucial processes such as growth, metabolism, and reproductive function. Loss-of-Function (LOF) mutations in the IGSF1 gene have been reported to cause the X-linked IGSF1 deficiency syndrome, a rare genetic condition that primarily affects males, characterized by hypothyroidism, macroorchidism, delayed puberty, obesity, and infertility. Case Report: In this study, we identified a novel hemizygous nonsense IGSF1 variant c.1989G>A (p.Trp663Ter) in a male patient who initially presented with growth impairment and growth hormone deficiency (GHD), with a positive family history on the maternal lineage. Notably, the proband does not present with macroorchidism, a feature typically associated with IGSF1 deficiency. The variant was also found in his heterozygous sister, who presented with isolated growth hormone deficiency, and in his mother, who displayed hypertension and thyroid dysfunction but no significant growth impairment. Discussion: This phenotypic variability suggests a differential expression of IGSF1-related symptoms depending on zygosity and sex within the same family, probably explained by X-chromosome inactivation (XCI) in females, which can lead to varying degrees of functional IGSF1 expression in different tissues. Conclusions: This case highlights the intrafamilial phenotypic variability associated with IGSF1 mutations, illustrating differences between male and female carriers and highlighting the importance of genetic testing in patients with similar clinical presentations. Full article

Background: Hypospadias development is influenced by prenatal androgen levels, with genetic factors typically playing a significant role. Through whole-exome sequencing, we found that rare damaging variants in DNAH8 (dynein axonemal heavy chain 8) were significantly enriched in hypospadias cases. However, the role of DNAH8 deficiency in hypospadias pathogenesis remains unclear. Objectives: This study aimed to clarify the function of DNAH8 in urethral development and fusion. Materials and Methods: Using CRISPR/Cas9, we generated DNAH8 knockout mice and employed a multi-disciplinary approach to evaluate urogenital development, male differentiation, testosterone levels, steroid biosynthesis gene expression, and cellular changes in fetal testes and external genitalia. Results:DNAH8 knockout mice presented abnormal masculinization phenotype, and fetal mice exhibited urethral fusion defects and hypoplastic glans during early urethral development. DNAH8 knockout was found to reduce prenatal testosterone levels and steroid biosynthesis in the testes. Based on single-cell sequencing and multicolor immunofluorescence, we demonstrated that in the early stage of fetal testis development, the loss of DNAH8 function affected the differentiation of Sertoli and steroidogenic cell lineages, thereby impairing testosterone synthesis ability during the masculinization programming window. Meanwhile, we identified two key distal glans cell populations that cause abnormal urethral fusion and hypoplastic glans. Furthermore, DNAH8 knockout could synergistically interact with low-dose endocrine-disrupting chemicals, increasing the incidence of urethral fusion defects at E16.5, and led to clear hypospadias phenotypes at E18.5. Conclusions: Loss of DNAH8 delays differentiation of Sertoli and steroidogenic lineages, reduces prenatal testosterone, and, with environmental exposure, increases hypospadias risk. Full article

Culter alburnus (topmouth culter, TC) is extensively distributed in various rivers and lakes in China. As a widely adaptive fish species, they have significant economic value and special ecological roles. Intergeneric hybridization is a pivotal strategy for generating novel hybrid lineages and species. In a previous study, we obtained an improved bisexual hybrid culter, BTBTF₁, derived from the hybrid lineage of Megalobrama amblycephala (blunt snout bream, BSB, 2n = 48, ♀) × Culter alburnus (2n = 48, ♂). In this study, we established an improved hybrid culter lineage by the self-crossing of BTBTF₁ and evaluated the biological characteristics regarding cytology, morphology, and genetics. DNA content and chromosome analyses confirmed that BTBTF₁-F₂ was a diploid lineage (2n = 48), with morphological traits exhibiting intermediate values between parental species, except for significantly TC-biased full-length-to-body length (FL/BL) and body length-to-head length (BL/HL) ratios (p < 0.05). ITS sequencing analysis revealed that BTBTF₁-F₂ inherited ITS1 sequences from BSB and TC. The global methylation level in BTBTF₁-F₂ was substantially reduced compared to progenitors, characterized by elevated full and diminished hemimethylation states. Transcriptomic analysis identified 7877 differentially expressed genes (DEGs), displaying 9.05%/8.30% maternal (BSB)-dominant and 17.01%/18.95% paternal (TC)-dominant expression patterns in BTBTF₁ and F₂. Remarkable intergenerational similarity in phenotypic and molecular profiles, coupled with bidirectional inheritance of progenitor characteristics, confirmed BTBTF₁-F₂ as a genetically stable allodiploid lineage. Remarkably, ITS sequencing analysis, methylation patterns, and DEG expression collectively demonstrated significant TC-oriented bias (p < 0.05). This study reports a novel stabilized allodiploid culter lineage after a comprehensive assessment at cytology, morphology, and genetic levels, and provides new insights into genetic bias in hybrid progeny. Full article

Background: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a congenital cardiac disorder, but its severity has been increasingly linked to inflammatory processes. This study aimed to investigate gene expression profiles in ARVC to identify genes potentially driving inflammation in affected individuals. Methods: Publicly available gene expression datasets comprising 12 ventricular tissue samples from six clinically confirmed ARVC patients (paired left and right ventricular biopsies) and 12 ventricular samples from six non-failing donor hearts were analyzed to identify differentially expressed genes. Immune infiltration was assessed to determine the proportions of immune cells in the ARVC condition. Correlation analysis between immune cell proportions and gene expression profiles was further performed to identify genes linked with inflammation-specific immune cells. Functional enrichment analysis of associated genes was performed to pinpoint the key involvement of genes in different inflammatory-specific pathways. Finally, the key gene associated with inflammation-specific immune cells and its active involvement in inflammatory pathways was further subjected to molecular docking against a curated library of marine-derived phytochemicals, followed by 100 ns molecular dynamics simulations to evaluate ligand stability. Results: A total of 141 significantly upregulated genes were identified in ARVC. Immune infiltration analysis revealed elevated proportions of regulatory T cells, CD8⁺ T cells, plasma cells, M2 macrophages, resting mast cells, and activated NK cells in the ARVC phenotype, indicating an immunologically active microenvironment. Correlation analysis identified four genes—LIFR, SCN2B, RGCC, and PIK3R1—showing significant positive associations with these immune cells. Functional enrichment analysis highlighted PIK3R1 (LogFC > 2.00) as a central regulator in the PI3K/AKT and mTOR pathways, which govern immune activation, cell survival, and fibrosis. Molecular docking identified two marine compounds, CMNPD18967 and CMNPD756, with strong binding affinities (−5.9 and −5.7 kcal/mol, respectively). Molecular dynamics simulations confirmed stable ligand binding within the PIK3R1 active site. Conclusions: PIK3R1 emerges as a key inflammation-associated gene in ARVC, with strong involvement in immune-regulatory pathways. Marine-derived phytochemicals CMNPD18967 and CMNPD756 demonstrate promising inhibitory potential through stable interaction with PIK3R1. While these findings present potential anti-inflammatory leads, validation in larger clinical cohorts and experimental models is essential to confirm translational applicability. Full article

Background: Biliary tract cancer (BTC) is an aggressive malignancy with poor prognosis and limited therapeutic options. Poly(ADP-ribose) polymerase (PARP) inhibitors have demonstrated efficacy in tumors with homologous recombination repair (HRR) deficiency. However, actionable BRCA1/2 mutations are rare in BTC. Epigenetic modulation via DNA methyltransferase (DNMT) inhibition is a proposed strategy for inducing an HR-deficient (“BRCAness”) phenotype and thereby enhancing therapeutic response to PARP inhibitors. This study aimed to determine whether the DNMT inhibitor azacitidine (AZA) enhances the antitumor effects of the PARP inhibitor niraparib (NIR) and to identify molecular mechanisms underlying this interaction. Methods: Two BTC cell lines, TFK-1 and RBE, were treated with AZA and/or NIR or subjected to siRNA-mediated DNMT1, DNMT3A, or DNMT3B knockdown. Functional analyses included homologous recombination (HR) assays, flow cytometric evaluation of cell-cycle distribution and apoptosis, proliferation and survival assays, and IC₅₀ determination. Whole-transcriptome RNA sequencing was performed to identify differentially expressed genes after AZA treatment or DNMT3B knockdown, followed by validation via qPCR and Western blotting. To explore epigenetic regulation, whole-genome bisulfite sequencing was performed on TFK-1 cells following DNMT3B knockdown. Results: AZA treatment decreased HR frequency in a dose-dependent manner and enhanced the sensitivity of BTC cells to NIR, as evidenced by increased apoptosis, suppressed proliferation, and reduced IC₅₀ values. DNMT3B knockdown recapitulated these effects, establishing a causal relationship between DNMT3B suppression and disrupted HR repair. RNA sequencing identified opioid growth factor receptor (OGFR) as a commonly upregulated gene after DNMT3B knockdown. Functional validation showed that OGFR overexpression reduced HR activity, increased apoptosis, and enhanced NIR sensitivity. Contrarily, OGFR knockdown conferred relative resistance. Whole-genome bisulfite sequencing showed no significant CpG methylation changes at the OGFR promoter region, indicating that OGFR induction is mediated through DNMT3B-dependent transcriptional regulation rather than direct promoter demethylation. Conclusions: DNMT3B inhibition sensitizes BTC cells to PARP inhibitors by disrupting HR repair. OGFR was identified as a novel regulator of HR and PARP inhibitor sensitivity, controlled via noncanonical DNMT3B-dependent transcriptional mechanisms that operate independently of CpG methylation. These findings provide new mechanistic insights into the epigenetic control of DNA repair and support the rationale for combining DNMT and PARP inhibitors as a promising therapeutic strategy for BTC beyond genetically HR-deficient cases. Full article

Codonopsis pilosula (Cp) is a traditional medicinal herb whose cultivation is limited by environmental factors like saline–alkali. Flavonoids, found in various plant organs, are involved in plant stress responses, but the specific saline–alkali stress response mechanism of Cp’s flavonoids is unknown. This study carried out saline–alkali stress treatments in Cp, collected samples from roots, stems, and leaves, and conducted physiological, biochemical, transcriptomic, and metabolomic tests. Phenotypic observations showed varying degrees of saline–alkali stress effects on different organs of Cp. Physiological tests revealed inconsistent antioxidant indicator changes across organs. Metabolomic and transcriptomic analyses revealed that, compared to roots and stems, leaves contained the highest number of differentially accumulated metabolites (DAMs) related to flavonoids, reaching up to 23, and harbored the most differentially expressed flavonoid-related genes, with up to 54; the roots treated with NaHCO₃ contained up to 14 types of flavonoids, while the leaves treated with NaHCO₃ contained up to 20 types of differentially expressed flavonoid-related genes; additionally, flavonoid pathway genes, including CHS, CHI, and bHLH transcription factors, might have responded to saline–alkali stress by modulating the production of flavonoid compounds such as Cyanidin and Galangin. This study preliminarily elucidated the molecular mechanisms of flavonoid response to saline–alkali stress in Cp, providing a theoretical basis for flavonoid exploitation, molecular breeding, and cultivation area expansion. Full article